.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.13.
.TH BDGBROADCALL "1" "December 2012" "bdgbroadcall 2.0.9.1" "User Commands"
.SH NAME
bdgbroadcall \- Fine-tuning script to call broad peaks from a single bedGraph track for scores
.SH SYNOPSIS
.B bdgbroadcall
\fI<-i bedGraph> \fR[\fI-c CUTOFF1\fR] [\fI-C CUTOFF2\fR] [\fI-l MIN\fR] [\fI-g MAX1\fR] [\fI-G MAX2\fR] [\fI-o PREFIX\fR]
.SH DESCRIPTION
Call broad peaks from MACS pvalue or qscore score bedGraph output, with
customized settings. Output two files for narrow peaks in encodePeak format,
and one for broad peaks in bed12 format.
.SH OPTIONS
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
Show this help message and exit.
.TP
\fB\-i\fR IFILE, \fB\-\-ifile\fR=\fIIFILE\fR
MACS pvalue score bedGraph
.TP
\fB\-c\fR CUTOFFPEAK, \fB\-\-cutoff\-peak\fR=\fICUTOFFPEAK\fR
Cutoff for peaks depending on which method you used
for score track. If the file contains qvalue scores
from MACS2, score 2 means qvalue 0.01. DEFAULT: 2
.TP
\fB\-C\fR CUTOFFLINK, \fB\-\-cutoff\-link\fR=\fICUTOFFLINK\fR
Cutoff for linking regions/low abundance regions
depending on which method you used for score track. If
the file contains qvalue scores from MACS2, score 1
means qvalue 0.1, and score 0.3 means qvalue 0.5.
DEFAULT: 5
.TP
\fB\-l\fR MINLEN, \fB\-\-min\-length\fR=\fIMINLEN\fR
minimum length of peak, better to set it as d value.
DEFAULT: 200
.TP
\fB\-g\fR LVL1MAXGAP, \fB\-\-lvl1\-max\-gap\fR=\fILVL1MAXGAP\fR
maximum gap between significant peaks, better to set
it as tag size. DEFAULT: 30
.TP
\fB\-G\fR LVL2MAXGAP, \fB\-\-lvl2\-max\-gap\fR=\fILVL2MAXGAP\fR
maximum linking between significant peaks, better to
set it as 4 times of d value. DEFAULT: 800
.TP
\fB\-o\fR OPREFIX, \fB\-\-o\-prefix\fR=\fIOPREFIX\fR
output file prefix, DEFAULT: peak